Testing methods: The evaluation of discovery operations in evolutionary biology

Cladistics

Volumn 18, Issue 1, 2002, Pages 94-111

  Grant, Taran ^a,b  

^a DIVISION OF INVERTEBRATE ZOOLOGY   (United States)

^b Howard Hughes Medical Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EVOLUTIONARY BIOLOGY;

EID: 0036213549     PISSN: 07483007     EISSN: None     Source Type: Journal    
DOI: 10.1006/clad.2002.0186     Document Type: Article

References (146)

1. Testing phylogenetic approaches with empirical data, as illustrated with the parsimony method
2. Data sets, partitions, and characters: Philosophies and procedures for analyzing multiple data sets
3. Are third positions really that bad? A test using vertebrate cytochrome b
4. Confirmation, semantics, and the interpretation of scientific theories
5. Evolution is not a necessary assumption of cladistics
6. Experimental molecular evolution of bacteriophage T7
7. Random cladistics
8. Towards simultaneous analysis of morphological and molecular data in Hymenoptera
9. What the tortoise said to Achilles
10. Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters
11. Species concepts and speciation analysis
12. Species concepts and the ontology of evolution
13. Intraspecific cladogram estimation: Accuracy at higher levels of divergence
14. Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods
15. Best-fit maximum likelihood models for phylogenetic inference: Empirical tests with known phylogenies
16. The general lineage concept of species, species criteria, and the process of speciation
17. A critique of the biological species concept and recommendations for a phylogenetic alternative
18. Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology
19. The meaning of relationship and taxonomic procedure
20. Simplicity and informativeness in systematics and phylogeny
21. The logical basis of phylogenetic analysis
22. On the boundaries of phylogenetic systematics
23. Phenetics in camouflage
24. Likelihood and inconsistency
25. Phylogenetic information content of five nuclear gene sequences in animals: Initial assessment of character sets from concordance and divergence studies
26. A nuclear gene for higher level phylogenetics: Phosphoenolpyruvate carboxykinase tracks Mesozoic-age divergences within Lepidoptera (Insecta)
27. Species, descriptive efficiency, and progress in systematics
28. Geographic variation, species recognition, and molecular evolution of cytochrome oxidase I in the Tropidurus spinulosus complex (Iguania: Tropiduridae)
29. Species in concept and practice: Herpetological applications
30. A consideration of epistemology in systematic biology, with special reference to species
31. Stability of cladistic relationships between Cetacea and higher-level artiodactyl taxa
32. An application of the theory of definitions to systematic principles
33. On psychologism in the logic of taxonomic controversies
34. Evaluating the phylogenetic utility of genes: A search for genes informative about deep divergences among vertebrates
35. On the foundations of biological systematics
36. Approaches for assessing phylogenetic accuracy
37. SINEs of the perfect character
38. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
39. Experimental phylogenetics: Generation of a known phylogeny
40. Experimental approaches to phylogenetic analysis
41. To tree the truth: Biological and numerical simulations of phylogeny
42. Application and accuracy of molecular phylogenies
43. Performance of phylogenetic methods in simulation
44. The robustness of two phylogenetic methods: Four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining
45. Success of phylogenetic methods in the four-taxon case
46. The operational imperative: Sense and nonsense in operationalism
47. When theories and methodologies clash: A phylogenetic reanalysis of the North American ambystomatid salamanders (Caudata: Ambystomatidae)
48. Improving accuracy of phylogenetic estimation by combining different methods
49. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae Serpentes)
50. Species as historical individuals
51. Testability and the refutation and corroboration of cladistic hypotheses
52. Total evidence or taxonomic congruence: Cladistics or consensus classification
53. The science of phylogenetic systematics: Explanation, prediction, and test
54. Parsimony with and without scientific justification
55. Testing the comparative method and lineage methods for inferring adaptation
56. Cladistics: What's in a word?
57. An empirical evaluation of the use of the ontogeny polarization criterion in phylogenetic inference
58. What does the comparative method reveal about adaptation?
59. What do population geneticists know and how do they know it?
60. Introduction: The pull of teleology
61. Substitution bias, weighted parsimony, and amniote phylogeny as inferred from 18S rRNA sequences
62. The biological species concept
63. The evidential significance of thought experiments in science
64. A test and review of the empirical performance of the ontogenetic criterion
65. Species concepts: A case for pluralism
66. Use of mitogenomic information in teleostean molecular phylogenetics: A tree-based exploration under the maximum-parsimony optimality criterion
67. A congruence test of reliability using linked mitochondrial DNA sequences
68. Testing species phylogenies and phylogenetic methods with congruence
69. In search of a method for cladistic biogeography: An empirical comparison of component analysis, Brooks parsimony analysis, and three-area statements
70. Issues in the logic of reductive explanations
71. Structural biology and phylogenetic estimation
72. Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences
73. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: Hippopotamuses are the closest living extant relatives of whales
74. On simultaneous analysis
75. An amplification of the phylogenetic species concept
76. Extinction and the origin of species
77. Systematic generalization, historical fate, and the species problem
78. Parsimony analysis of total evidence from extinct and extant taxa and the cetacean - Artiodactyls question (Mammalia, Ungulata)
79. The position of Cetacea within Mammalia: Phylogenetic analysis of morphological data from extinct and extant taxa
80. Progress in methods for constructing evolutionary trees
81. Philosophy and the transformation of cladistics
82. Biases in maximum likelihood and parsimony: A simulation approach to a ten-taxon case
83. A deductive-nomological model of probabilistic explanation
84. Vicariant patterns and historical explanation in biogeography
85. Fishes from the uplands and intermontane basins of Guatemala: Revisionary studies and comparative geography
86. Laws, history, and the nature of biological understanding
87. Reductionism in a historical science
88. Falsifiability, consilience, and systematics
89. Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny
90. Relative efficiencies of the Fitch-Margoliash, maximum-parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree
91. The neighbor-joining method: A new method for reconstructing phylogenetic trees
92. The effect of male coloration on female mate choice in closely related Lake Victoria cichlids (Haplochromis nyererei complex)
93. Cichlid fish diversity threatened by eutrophication that curbs sexual selection
94. Success of parsimony in the four-taxon case: Long-branch repulsion by likelihood in the Farris zone
95. Probabilism and phylogenetic inference
96. Letter to the editor
97. Experimental tests of phylogenetic inference methods
98. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree
99. Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site
100. Links between maximum likelihood and maximum parsimony under a simple model of site substitution
101. Homoplasy: The result of natural selection, or evidence of design limitations?
102. Theories, models and constraints
103. When is a phylogenetic test good enough?
104. Comparing methods: Adaptive traits and tests of adaptation
105. Noise
106. Ontogeny and character phylogeny
107. Another way of looking at the species problem: A reply to de Queiroz and Donoghue
108. Polymorphic characters in phylogenetic systematics
109. Testing phylogenetic methods with tree congruence: Phylogenetic analysis of polymorphic morphological characters in phrynosomatid lizards
110. Reconstructing phylogenies from allozyme data: Comparing method performance with congruence
111. Popper, systematics, and classifications: A reply to Walter Bock and other evolutionary taxonomists
112. The phylogeny and biogeography of fossil and recent gars (Actinopterygii: Lepsisosteidae)
113. The evolutionary species concept reconsidered
114. The evolutionary species concept
115. Recovery of cichlid species in Lake Victoria: An examination of factors leading to differential extinction
116. Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites
117. Phylogenetic analysis using parsimony and maximum likelihood methods
118. On the best evolutionary rate for phylogenetic analysis
119. Complexity of the simplest phylogenetic problem
120. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates